Saccharibacteria, formerly known as ''TM7'', is a major bacterial lineage. It was discovered through

16S rRNA 16S ribosomal RNA (or 16Svedberg, S rRNA) is the RNA component of the 30S subunit of a prokaryotic ribosome (SSU rRNA). It binds to the Shine-Dalgarno sequence and provides most of the SSU structure. The genes coding for it are referred to as ...

sequencing . TM7x from the human oral cavity was cultivated and revealed that TM7x is an extremely small

coccus Bacterial cellular morphologies are the shapes that are characteristic of various types of bacteria and often key to their identification. Their direct examination under a light microscope enables the classification of these bacteria (and archaea ...

(200-300 nm) and has a distinctive lifestyle not previously observed in human-associated microbes. It is an obligate

epibiont An epibiont (from the Ancient Greek meaning "living on top of") is an organism that lives on the surface of another living organism, called the basibiont ("living underneath"). The interaction between the two organisms is called epibiosis. An ep ...

of various hosts, including ''

Actinomyces ''Actinomyces'' is a genus of the Actinomycetia class of bacteria. They all are Gram-positive and facultatively anaerobic, growing best under anaerobic conditions. ''Actinomyces'' species may form endospores, and while individual bacteria are r ...

odontolyticus'' strain (XH001) yet also has a

parasitic Parasitism is a close relationship between species, where one organism, the parasite, lives (at least some of the time) on or inside another organism, the host, causing it some harm, and is adapted structurally to this way of life. The ent ...

phase thereby killing its host. The full genome sequence revealed a highly reduced genome (705kB) and a complete lack of amino acid biosynthetic capacity. An axenic culture of TM7 from the oral cavity was reported in 2014 but no sequence or culture was made available. Along with Candidate Phylum TM6, it was named after sequences obtained in 1994 in an environmental study of a soil sample of peat bog in Germany where 262 PCR amplified 16S rDNA fragments were cloned into a

plasmid A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria and ...

vector, named TM clones for ' ( lit. peat, middle layer). It has been found in several environments since such as from

activated sludge The activated sludge process is a type of biological wastewater treatment process for treating sewage or Industrial wastewater treatment, industrial wastewaters using aeration and a biological floc (biofilm), floc composed of bacteria and protozoa ...

water treatment Water treatment is any process that improves the quality of water to make it appropriate for a specific end-use. The end use may be drinking, industrial water supply, irrigation, river flow maintenance, water recreation or many other uses, ...

plant sludge

rainforest Rainforests are forests characterized by a closed and continuous tree Canopy (biology), canopy, moisture-dependent vegetation, the presence of epiphytes and lianas and the absence of wildfire. Rainforests can be generally classified as tropi ...

soil, human

saliva Saliva (commonly referred as spit or drool) is an extracellular fluid produced and secreted by salivary glands in the mouth. In humans, saliva is around 99% water, plus electrolytes, mucus, white blood cells, epithelial cells (from which ...

, in association with

sponge Sponges or sea sponges are primarily marine invertebrates of the animal phylum Porifera (; meaning 'pore bearer'), a basal clade and a sister taxon of the diploblasts. They are sessile filter feeders that are bound to the seabed, and a ...

cockroach Cockroaches (or roaches) are insects belonging to the Order (biology), order Blattodea (Blattaria). About 30 cockroach species out of 4,600 are associated with human habitats. Some species are well-known Pest (organism), pests. Modern cockro ...

es,

gold mines Gold mining is the extraction of gold by mining. Historically, mining gold from alluvial deposits used manual separation processes, such as gold panning. The expansion of gold mining to ores that are not on the surface has led to more complex ...

acetate An acetate is a salt formed by the combination of acetic acid with a base (e.g. alkaline, earthy, metallic, nonmetallic, or radical base). "Acetate" also describes the conjugate base or ion (specifically, the negatively charged ion called ...

-amended

aquifer An aquifer is an underground layer of water-bearing material, consisting of permeability (Earth sciences), permeable or fractured rock, or of unconsolidated materials (gravel, sand, or silt). Aquifers vary greatly in their characteristics. The s ...

sediment, and other environments (bar

thermophilic A thermophile is a type of extremophile that thrives at relatively high temperatures, between . Many thermophiles are archaea, though some of them are bacteria and fungi. Thermophilic eubacteria are suggested to have been among the earliest bact ...

), making it an abundant and widespread phylum. Recently, TM7 rDNA and whole-cells were detected in activated sludge with >99.7% identity to a human skin TM7 and 98.6% identity to the human oral TM7a, suggesting metabolically active TM7 isolates in environmental sites may serve as model organisms to investigate the role TM7 species play in human health.

Properties

TM7 specific

FISH A fish (: fish or fishes) is an aquatic animal, aquatic, Anamniotes, anamniotic, gill-bearing vertebrate animal with swimming fish fin, fins and craniate, a hard skull, but lacking limb (anatomy), limbs with digit (anatomy), digits. Fish can ...

probes identified species from a

bioreactor A bioreactor is any manufactured device or system that supports a biologically active environment. In one case, a bioreactor is a vessel in which a chemical reaction, chemical process is carried out which involves organisms or biochemistry, biochem ...

sludge revealed the presence of a

gram-positive In bacteriology, gram-positive bacteria are bacteria that give a positive result in the Gram stain test, which is traditionally used to quickly classify bacteria into two broad categories according to their type of cell wall. The Gram stain is ...

cell envelopes and several morphotypes: a sheathed

filament The word filament, which is descended from Latin ''filum'' meaning " thread", is used in English for a variety of thread-like structures, including: Astronomy * Galaxy filament, the largest known cosmic structures in the universe * Solar filament ...

(abundant), a rod occurring in short chains, a thick filament and cocci; the former may be the cause of Eikelboom type 0041 (bulking problems of activated sludges). The majority of

bacterial phyla Bacterial phyla constitute the major lineages of the domain Bacteria. While the exact definition of a bacterial phylum is debated, a popular definition is that a bacterial phylum is a monophyletic lineage of bacteria whose 16S rRNA genes share ...

are

Gram-negative Gram-negative bacteria are bacteria that, unlike gram-positive bacteria, do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. Their defining characteristic is that their cell envelope consists ...

diderms, whereas only the

Bacillota The Bacillota (synonym Firmicutes) are a phylum of bacteria, most of which have Gram-positive cell wall structure. They have round cells, called cocci (singular coccus), or rod-like forms (bacillus). A few Bacillota, such as '' Megasphaera'', ...

, the

Actinomycetota The Actinomycetota (or Actinobacteria) are a diverse phylum of Gram-positive bacteria with high GC content. They can be terrestrial or aquatic. They are of great importance to land flora because of their contributions to soil systems. In soil t ...

and

Chloroflexota The Chloroflexota are a phylum of bacteria containing isolates with a diversity of phenotypes, including members that are aerobic thermophiles, which use oxygen and grow well in high temperatures; anoxygenic phototrophs, which use light for ph ...

are monoderms. Using a

polycarbonate Polycarbonates (PC) are a group of thermoplastic polymers containing carbonate ester, carbonate groups in their chemical structures. Polycarbonates used in engineering are strong, toughness, tough materials, and some grades are optically transp ...

membrane as a growth support and soil extract as the substrate, microcolonies of this clade were grown consisting of long filamentous rods up to 15 μm long with less than 50 cells or short rods with several hundred cells per colony, after 10 days incubation. Thanks to a microfluidic chip allowing the isolation and amplification of the genome of a single cell, the genome of 3 long filament morphology cells with identical 16S rRNA were sequenced to create a draft sequence of the genome confirming some previously ascertained properties, elucidating some of its metabolic capabilities, revealing novel genes and hinting to potential pathogenic abilities. Over 50 different phylotypes have been identified and it has a relatively modest intradivision 16S rDNA sequence divergence of 17%, which ranges from 13 to 33%. An interactive

phylogenetic tree A phylogenetic tree or phylogeny is a graphical representation which shows the evolutionary history between a set of species or taxa during a specific time.Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA. In ...

of TM7, built using jsPhyloSVG, allows for quick access to

GenBank The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. It is produced and maintained by the National Center for Biotechnology Information (NCBI; a par ...

sequences and distance matrix calculations between tree branches. Stable-isotope probing studies have found that some members of this phylum can degrade

toluene Toluene (), also known as toluol (), is a substituted aromatic hydrocarbon with the chemical formula , often abbreviated as , where Ph stands for the phenyl group. It is a colorless, water Water is an inorganic compound with the c ...

Taxonomy

The currently accepted taxonomy is based on the

List of Prokaryotic names with Standing in Nomenclature List of Prokaryotic names with Standing in Nomenclature (LPSN) is an online database that maintains information on the naming and taxonomy of prokaryotes, following the taxonomy requirements and rulings of the International Code of Nomenclatu ...

(LPSN) and

National Center for Biotechnology Information The National Center for Biotechnology Information (NCBI) is part of the National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The NCBI is lo ...

(NCBI) * Class "Saccharimonadia" corrig. McLean et al. 2020 corrig. McLean et al. 2020; "Nanosyncoccia" corrig. McLean et al. 2020">Nanoperiodontomorbia" corrig. McLean et al. 2020; "Nanosyncoccia" corrig. McLean et al. 2020** Order "Saccharimonadales" McLean et al. 2020 ["Nanogingivalales" corrig. McLean et al. 2020; "Nanoperiodontomorbales" corrig. McLean et al. 2020; "Nanosynbacterales" McLean et al. 2020; "Nanosyncoccales" McLean et al. 2020] *** ?"''Ca.'' Minimicrobia" Ibrahim et al. 2021 **** "''Ca.'' M. naudis" Ibrahim et al. 2021 **** "''Ca.'' M. vallesae" Ibrahim et al. 2021 *** ?"''Ca.'' Nanosynsaccharibacterium" corrig. McLean et al. 2020 *** ?"''Ca.'' Southlakia" Wang et al. 2023 **** "''Ca.'' S. epibionticum" Wang et al. 2023 *** Family AMD01 **** "''Ca.'' Chaera" corrig. Lemos et al. 2019 ***** "''Ca.'' C. renei" corrig. Lemos et al. 2019 *** Family "Nanoperiodontomorbaceae" corrig. McLean et al. 2020 **** "''Ca.'' Nanoperiodontomorbus" corrig. McLean et al. 2020 ***** "''Ca.'' N. periodonticus" corrig. McLean et al. 2020 *** Family "Nanogingivalaceae" McLean et al. 2020 **** "''Ca.'' Nanogingivalis" McLean et al. 2020 ***** "''Ca.'' N. gingivitcus" McLean et al. 2020 *** Family "Nanosyncoccaceae" McLean et al. 2020 **** "''Ca.'' Nanosyncoccus" McLean et al. 2020 ***** ?"''Ca.'' N. oralis" Gilroy et al. 2023 ***** "''Ca.'' N. alces" McLean et al. 2020 ***** "''Ca.'' N. nanoralicus" McLean et al. 2020 *** Family UBA1547 **** "''Ca.'' Microsaccharimonas" corrig. Lemos et al. 2019 Lemos et al. 2019 non Jojima et al. 2004">Candidatus Saccharibacter" Lemos et al. 2019 non Jojima et al. 2004(AMD02) ***** "''Ca.'' M. sossegonensis" corrig. Lemos et al. 2019 *** Family UBA10027 **** "''Ca.'' Mycolatisynbacter" corrig. Batinovic et al. 2021 Batinovic et al. 2021">''Ca.'' Mycosynbacter" Batinovic et al. 2021(JR1) ***** "''Ca.'' M. gordoniilyticus" corrig. Batinovic et al. 2021 Batinovic et al. 2021">''Ca.'' Mycosynbacter amalyticus" Batinovic et al. 2021*** Family "Saccharimonadaceae" McLean et al. 2020 **** "''Ca.'' Saccharimonas" Albertsen et al. 2013 ***** "''Ca.'' S. aalborgensis" Albertsen et al. 2013 *** Family "Nanosynbacteraceae" McLean et al. 2020 **** "''Ca.'' Nanosynbacter" McLean et al. 2020 (TM7x) ***** ?"''Ca.'' N. colneyensis" Gilroy et al. 2023 ***** ?"''Ca.'' N. gullae" Gilroy et al. 2023 ***** ?"''Ca.'' N. norwichensis" Gilroy et al. 2023 ***** ?"''Ca.'' N. quadrami" Gilroy et al. 2023 ***** "''Ca.'' N. featherlites" McLean et al. 2020 ***** "''Ca.'' N. lyticus" McLean et al. 2020

References

Fredrik Bäckhed, Ruth Ley, Justin L Sonnenburg, Daniel A. Peterson, Jeffrey I. Gordon
Host‐Bacterial Mutualism in the Human Intestine
In: Science 307(5717): 1915-1920. April 2005. doi:10.1126/science.1104816. Michael A. Dojka, Philip Hugenholtz, Sheridan K. Haack, Norman R. Pace
Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation
In: ASM Appl. Environ. Microbiol. 64(10): 3869-3877. 29 October 2020. doi:10.1128/AEM.64.10.3869-3877.1998. PMID 9758812. Damien M. de Vienne
Parcubacteria group
NCBI Lifemap,

University of Lyon The University of Lyon ( , or UdL) is a university system ( ''ComUE'') based in Lyon, France. It comprises 12 members and 9 associated institutions. The 3 main constituent universities in this center are: Claude Bernard University Lyon 1, which f ...

. Lifemap is an interactive tool to explore NCBI taxonomy. Damien M. de Vienne
environmental samples - candidate division WS5
NCBI Lifemap,

. Lifemap is an interactive tool to explore NCBI taxonomy. C. L. Schoch, Sayers ''et al''.
Parcubacteria groupParcubacteria group
(clade/superphylum, syn. candidate division OD1); C. L. Schoch, Sayers ''et al''.
candidate division WS5candidate division WS5
(clade, syn. candidate division Wurtsmith 5);

External links

Ultra-Small, Parasitic Bacteria Found in Groundwater, Dogs, Cats — And You
on: SciTechDaily; July 21, 2020; source: Forsyth Institute * Jeffrey S. McLean, Batbileg Bor, Kristopher A. Kerns, Kelly Wrighton, Wenyuan Shi, Xuesong He, ''et al.''
Acquisition and Adaptation of Ultra-small Parasitic Reduced Genome Bacteria to Mammalian Hosts
in: CellRep 32, 107939; July 21, 2020; doi:10.1016/j.celrep.2020.107939 * Jeffrey S. McLean, Batbileg Bor, Thao T. To, Quanhui Liu, Kristopher A. Kerns, Lindsey Solden, Kelly Wrighton, Xuesong He, Wenyuan Shi
Evidence of independent acquisition and adaption of ultra-small bacteria to human hosts across the highly diverse yet reduced genomes of the phylum Saccharibacteria
on: bioRxiv; February 02, 2018; doi:10.1101/258137 (PrePrint) {{Taxonbar, from=Q5031741 Bacteria Bacteria phyla Candidatus taxa

Properties

Taxonomy

See also

References

External links